A concise synthesis of protected 5-cyano-L-tryptophan (Trp5CN) has been developed for 2D IR spectroscopic investigations within peptides or proteins. To assess the potential of differently substituted cyano-tryptophans, several model cyanoindole systems were characterized using IR spectroscopy. Upon assessment of their spectroscopic properties, Trp5CN was integrated into a model peptide sequence, Trp5CN–Gly–Phe4CN, to elucidate its structure. This peptide demonstrates the capability of this probe, Trp5CN and Phe4CN, to capture structural information via 2D IR spectroscopy. The 2D IR spectrum of the peptide in water was simulated to reveal a unique spectral signature resulting from the presence of dipolar coupling. The coupling strength between cyano-labels was determined to be 1.4 cm−1 by matching the slopes along the max contour between the simulated and experimental spectrum. Using transition dipole coupling, a distance between the two probes of 13 Å was calculated.